Currently, when running prodigal, prokka automatically sets anonymous (formerly metagenome) mode when the total input sequences are shorter than 100,000 bases. If a training file is specified with the --prodigaltf option, it is ignored by prodigal because of this.
The current patch changes the behavior to not set anonymous mode if a training file is specified, regardless of input length. It also adds a check to make sure the prodigal file is readable, and croaks if not (currently this is silently ignored).
Currently, when running prodigal, prokka automatically sets anonymous (formerly metagenome) mode when the total input sequences are shorter than 100,000 bases. If a training file is specified with the
--prodigaltfoption, it is ignored by prodigal because of this.The current patch changes the behavior to not set anonymous mode if a training file is specified, regardless of input length. It also adds a check to make sure the prodigal file is readable, and croaks if not (currently this is silently ignored).